Taking benefit of the AlpArray temporary network and permanent networks in W‐Europe, we construct a 3‐D onshore‐offshore velocity model of the crust and upper mantle using ambient‐noise wave‐equation tomography. We use a frequency‐dependent phase traveltime misfit function in an iterative procedure to refine a recent 3‐D Vs model computed from a Bayesian two‐step ambient noise tomography. Observed waveforms consist of vertical‐component noise correlations from 600 broadband stations in the Alps and surroundings, including ocean‐bottom seismometers in the Ligurian sea. We perform 3‐D inversion in the 5–85 s period range. In the long‐period band (20–85 s), an elastic approximation is considered, while in the 5–20 s band, we account for the effect of water layer in the Ligurian sea by applying a fluid‐solid coupling for acoustic‐elastic waveform simulations. The resulting Vs model enhances the shape and contrast of velocity structures, accounting for 3‐D and finite‐frequency effects. It emphasizes the deep sediments of the Ligurian‐Provence basin and focuses on the low‐velocity anomalies of the crust in the W‐Alps. We obtain a high‐resolution Moho depth map covering the Alps and Ligurian sea. In the W‐Alps, this map confirms the deepening of the European crust following the subduction beneath Adria and the existence of major structures such as the Moho jump beneath the external crystalline massifs and shallow depths associated with the Ivrea Body. It provides further constraints on the deep structure beneath the Ligurian‐Provence basin, regarding the lateral and along‐strike crustal‐thickness variations from the oceanic domain to the conjugate margins.